The error estimation of guidance radar is a foundation and prerequisite for information sharing among radar stations. Aimed at the error estimation of radar station without reference data, the niche genetic algorithm is adopted to solve the difficulties. Compared to the traditional genetic algorithm, the use of the niche genetic algorithm can overcome the shortcomings of premature convergence and slow convergence rate at ending. The simulation and the project practice show that the algorithm is reasonable and feasible. The guidance radar's error margin estimation plays an important role in the coordination among radar stations.